Harvest for Moseley 1885 Created 19 Apr 15:44

Stage: completed
Fetched: 19 Apr 15:44
Validated: 19 Apr 15:44
Deltas Created 19 Apr 15:44
Units Normalized: 19 Apr 15:44
Ancestry Built: 19 Apr 15:44
Nodes Matched: 19 Apr 15:44
Names Parsed: 19 Apr 15:44
New Models Stored: 19 Apr 15:44
Indexed: 19 Apr 15:44
Completed: 19 Apr 15:45
Time to Harvest: less than a minute

Harvesting Log

(687 lines)
# Logfile created on 2020-08-27 15:45:19 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:45:19] logged process
[START] [2020-08-27 15:45:19] Creating resource from OpenData
[START] [2020-08-27 15:45:19] logged process
[START] [2020-08-27 15:45:19] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:45:19] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:45:19] Creating resource from OpenData
[INFO] [2020-12-03 11:41:32] ## HARVEST: type = -harvest
[START] [2020-12-03 11:41:36] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 11:41:36] create_harvest_instance
[STOP] [2020-12-03 11:41:38] create_harvest_instance
[START] [2020-12-03 11:41:38] fetch_files
[STOP] [2020-12-03 11:41:38] fetch_files
[START] [2020-12-03 11:41:38] validate_each_file
[STOP] [2020-12-03 11:41:38] validate_each_file
[START] [2020-12-03 11:41:38] convert_to_csv
[CMD] [2020-12-03 11:41:38] /usr/bin/sort /app/public/converted_csv/moseley_moseley__refs_24836.csv > /app/public/converted_csv/moseley_moseley__refs_24836.csv_sorted
[CMD] [2020-12-03 11:41:38] /usr/bin/sort /app/public/converted_csv/moseley_moseley__nodes_24837.csv > /app/public/converted_csv/moseley_moseley__nodes_24837.csv_sorted
[CMD] [2020-12-03 11:41:38] /usr/bin/sort /app/public/converted_csv/moseley_moseley__occurrences_24838.csv > /app/public/converted_csv/moseley_moseley__occurrences_24838.csv_sorted
[CMD] [2020-12-03 11:41:38] /usr/bin/sort /app/public/converted_csv/moseley_moseley__measurements_24839.csv > /app/public/converted_csv/moseley_moseley__measurements_24839.csv_sorted
[STOP] [2020-12-03 11:41:38] convert_to_csv
[START] [2020-12-03 11:41:38] calculate_delta
[CMD] [2020-12-03 11:41:38] echo "0a" > /app/public/diff/moseley_moseley__refs_24836.diff
[CMD] [2020-12-03 11:41:38] tail -n +1 /app/public/converted_csv/moseley_moseley__refs_24836.csv >> /app/public/diff/moseley_moseley__refs_24836.diff
[CMD] [2020-12-03 11:41:38] echo "." >> /app/public/diff/moseley_moseley__refs_24836.diff
[CMD] [2020-12-03 11:41:38] echo "0a" > /app/public/diff/moseley_moseley__nodes_24837.diff
[CMD] [2020-12-03 11:41:38] tail -n +1 /app/public/converted_csv/moseley_moseley__nodes_24837.csv >> /app/public/diff/moseley_moseley__nodes_24837.diff
[CMD] [2020-12-03 11:41:38] echo "." >> /app/public/diff/moseley_moseley__nodes_24837.diff
[CMD] [2020-12-03 11:41:38] echo "0a" > /app/public/diff/moseley_moseley__occurrences_24838.diff
[CMD] [2020-12-03 11:41:38] tail -n +1 /app/public/converted_csv/moseley_moseley__occurrences_24838.csv >> /app/public/diff/moseley_moseley__occurrences_24838.diff
[CMD] [2020-12-03 11:41:38] echo "." >> /app/public/diff/moseley_moseley__occurrences_24838.diff
[CMD] [2020-12-03 11:41:38] echo "0a" > /app/public/diff/moseley_moseley__measurements_24839.diff
[CMD] [2020-12-03 11:41:38] tail -n +1 /app/public/converted_csv/moseley_moseley__measurements_24839.csv >> /app/public/diff/moseley_moseley__measurements_24839.diff
[CMD] [2020-12-03 11:41:38] echo "." >> /app/public/diff/moseley_moseley__measurements_24839.diff
[STOP] [2020-12-03 11:41:38] calculate_delta
[START] [2020-12-03 11:41:38] parse_diff_and_store
[INFO] [2020-12-03 11:41:38] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:41:38] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:41:38] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:41:38] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:41:39] Storing 6 ScientificNames
[INFO] [2020-12-03 11:41:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-03 11:41:39] Average Time: 0.01
[INFO] [2020-12-03 11:41:39] Total Time: 1s
[INFO] [2020-12-03 11:41:39] Storing 6 Nodes
[INFO] [2020-12-03 11:41:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-03 11:41:39] Average Time: 0.01
[INFO] [2020-12-03 11:41:39] Total Time: 1s
[INFO] [2020-12-03 11:41:39] Storing 6 Occurrences
[INFO] [2020-12-03 11:41:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-03 11:41:39] Average Time: 0.0
[INFO] [2020-12-03 11:41:39] Total Time: 1s
[INFO] [2020-12-03 11:41:39] Storing 22 Traits
[INFO] [2020-12-03 11:41:39] Processing group of 22 in 1 groups of 1000
[INFO] [2020-12-03 11:41:39] Average Time: 0.01
[INFO] [2020-12-03 11:41:39] Total Time: 1s
[INFO] [2020-12-03 11:41:39] Storing 11 MetaTraits
[INFO] [2020-12-03 11:41:39] Processing group of 11 in 1 groups of 1000
[INFO] [2020-12-03 11:41:39] Average Time: 0.0
[INFO] [2020-12-03 11:41:39] Total Time: 1s
[STOP] [2020-12-03 11:41:39] parse_diff_and_store
[START] [2020-12-03 11:41:39] resolve_keys
[INFO] [2020-12-03 11:41:45] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:41:45] traits to occurrences...
[INFO] [2020-12-03 11:41:45] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:41:45] Traits to sex term...
[INFO] [2020-12-03 11:41:45] Traits to lifestage term...
[INFO] [2020-12-03 11:41:45] MetaTraits to traits...
[INFO] [2020-12-03 11:41:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:41:45] Assocs to occurrences...
[INFO] [2020-12-03 11:41:45] Assocs to nodes...
[INFO] [2020-12-03 11:41:45] Assoc to sex term...
[INFO] [2020-12-03 11:41:45] Assoc to lifestage term...
[INFO] [2020-12-03 11:41:45] MetaAssoc to assocs...
[STOP] [2020-12-03 11:41:45] resolve_keys
[START] [2020-12-03 11:41:45] hold_for_later_1
[STOP] [2020-12-03 11:41:45] hold_for_later_1
[START] [2020-12-03 11:41:45] hold_for_later_2
[STOP] [2020-12-03 11:41:45] hold_for_later_2
[START] [2020-12-03 11:41:45] resolve_missing_parents
[STOP] [2020-12-03 11:41:45] resolve_missing_parents
[START] [2020-12-03 11:41:45] rebuild_nodes
[START] [2020-12-03 11:41:45] Flattener#flatten
[START] [2020-12-03 11:41:45] Flattener#study_resource
[START] [2020-12-03 11:41:45] Flattener#build_ancestry
[STOP] [2020-12-03 11:41:45] Flattener#build_ancestry
[INFO] [2020-12-03 11:41:45] 6 ancestry keys
[START] [2020-12-03 11:41:45] build_node_ancestors
[INFO] [2020-12-03 11:41:45] old ancestors deleted.
[STOP] [2020-12-03 11:41:45] build_node_ancestors
[WARN] [2020-12-03 11:41:45] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:41:45] Flattener#flatten
[STOP] [2020-12-03 11:41:45] rebuild_nodes
[START] [2020-12-03 11:41:45] resolve_missing_media_owners
[STOP] [2020-12-03 11:41:45] resolve_missing_media_owners
[START] [2020-12-03 11:41:45] sanitize_media_verbatims
[STOP] [2020-12-03 11:41:45] sanitize_media_verbatims
[START] [2020-12-03 11:41:45] queue_downloads
[STOP] [2020-12-03 11:41:45] queue_downloads
[START] [2020-12-03 11:41:45] parse_names
[WARN] [2020-12-03 11:41:45] I see 6 names which still need to be parsed.
[STOP] [2020-12-03 11:41:46] parse_names
[START] [2020-12-03 11:41:46] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:41:46] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:41:46] match_nodes
[START] [2020-12-03 11:41:46] map_all_nodes_to_pages
[STOP] [2020-12-03 11:41:46] map_all_nodes_to_pages
[INFO] [2020-12-03 11:41:46] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2020-12-03 11:41:46] update_nodes
[STOP] [2020-12-03 11:41:46] update_nodes
[STOP] [2020-12-03 11:41:46] match_nodes
[START] [2020-12-03 11:41:46] reindex_search
[STOP] [2020-12-03 11:41:46] reindex_search
[START] [2020-12-03 11:41:46] normalize_units
[STOP] [2020-12-03 11:41:46] normalize_units
[START] [2020-12-03 11:41:46] calculate_statistics
[2020-12-03 11:41:46] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:41:46] calculate_statistics
[START] [2020-12-03 11:41:46] complete_harvest_instance
[START] [2020-12-03 11:41:46] overall_tsv_creation
[INFO] [2020-12-03 11:41:46] Processing group of 6 in 1 batches of 10000
[INFO] [2020-12-03 11:42:25] 6 Traits (unfiltered)...
[INFO] [2020-12-03 11:43:04] 6 Traits (filtered)...
[INFO] [2020-12-03 11:43:04] 0 Associations (filtered)...
[INFO] [2020-12-03 11:43:04] 27 metadata added.
[INFO] [2020-12-03 11:43:04] 0 metadata added.
[INFO] [2020-12-03 11:43:04] Average Time: 55.03
[INFO] [2020-12-03 11:43:04] Total Time: 1m18s
[STOP] [2020-12-03 11:43:04] overall_tsv_creation
[INFO] [2020-12-03 11:43:04] Done. Check your files:
[INFO] [2020-12-03 11:43:04] (6 lines) /app/public/data/moseley_moseley_/publish_nodes.tsv
[INFO] [2020-12-03 11:43:04] (6 lines) /app/public/data/moseley_moseley_/publish_scientific_names.tsv
[INFO] [2020-12-03 11:43:04] (7 lines) /app/public/data/moseley_moseley_/publish_traits.tsv
[INFO] [2020-12-03 11:43:04] (28 lines) /app/public/data/moseley_moseley_/publish_metadata.tsv
[STOP] [2020-12-03 11:43:04] complete_harvest_instance
[START] [2020-12-03 11:43:04] completed
[STOP] [2020-12-03 11:43:04] completed
[STOP] [2020-12-03 11:43:04] logged process, took 87.81
[INFO] [2020-12-03 11:51:28] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-12-03 11:51:31] ## remove_type: ScientificName
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 6 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.061] Removed 6 Scientificnames
[INFO] [2020-12-03 11:51:31] ## remove_type: Vernacular
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.064] Removed 0 Vernaculars
[INFO] [2020-12-03 11:51:31] ## remove_type: Article
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.067] Removed 0 Articles
[INFO] [2020-12-03 11:51:31] ## remove_type: Medium
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.071] Removed 0 Media
[INFO] [2020-12-03 11:51:31] ## remove_type: Trait
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 22 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.075] Removed 22 Traits
[INFO] [2020-12-03 11:51:31] ## remove_type: MetaTrait
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 11 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.078] Removed 11 Metatraits
[INFO] [2020-12-03 11:51:31] ## remove_type: OccurrenceMetadatum
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.081] Removed 0 Occurrencemetadata
[INFO] [2020-12-03 11:51:31] ## remove_type: Assoc
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.083] Removed 0 Assocs
[INFO] [2020-12-03 11:51:31] ## remove_type: MetaAssoc
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.086] Removed 0 Metaassocs
[INFO] [2020-12-03 11:51:31] ## remove_type: Identifier
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.088] Removed 0 Identifiers
[INFO] [2020-12-03 11:51:31] ## remove_type: Reference
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.091] Removed 0 References
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] Starting batch with ID 86116140...
[INFO] [2020-12-03 11:51:31] ## remove_type: Node
[INFO] [2020-12-03 11:51:31] ++ Calling delete_all on 6 instances...
[INFO] [2020-12-03 11:51:31] [11:51:31.927] Removed 6 Nodes
[START] [2020-12-03 11:51:32] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 11:51:32] Creating resource from OpenData
[START] [2020-12-03 11:51:32] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 11:51:32] Parse meta.xml file and create formats with fields
[STOP] [2020-12-03 11:51:32] Parse meta.xml file and create formats with fields
[STOP] [2020-12-03 11:51:32] Creating resource from OpenData
[START] [2020-12-03 11:51:32] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 11:51:32] create_harvest_instance
[STOP] [2020-12-03 11:51:34] create_harvest_instance
[START] [2020-12-03 11:51:34] fetch_files
[STOP] [2020-12-03 11:51:34] fetch_files
[START] [2020-12-03 11:51:34] validate_each_file
[STOP] [2020-12-03 11:51:34] validate_each_file
[START] [2020-12-03 11:51:34] convert_to_csv
[CMD] [2020-12-03 11:51:34] /usr/bin/sort /app/public/converted_csv/moseley_moseley__refs_24848.csv > /app/public/converted_csv/moseley_moseley__refs_24848.csv_sorted
[CMD] [2020-12-03 11:51:34] /usr/bin/sort /app/public/converted_csv/moseley_moseley__nodes_24849.csv > /app/public/converted_csv/moseley_moseley__nodes_24849.csv_sorted
[CMD] [2020-12-03 11:51:34] /usr/bin/sort /app/public/converted_csv/moseley_moseley__occurrences_24850.csv > /app/public/converted_csv/moseley_moseley__occurrences_24850.csv_sorted
[CMD] [2020-12-03 11:51:34] /usr/bin/sort /app/public/converted_csv/moseley_moseley__measurements_24851.csv > /app/public/converted_csv/moseley_moseley__measurements_24851.csv_sorted
[STOP] [2020-12-03 11:51:34] convert_to_csv
[START] [2020-12-03 11:51:34] calculate_delta
[CMD] [2020-12-03 11:51:34] echo "0a" > /app/public/diff/moseley_moseley__refs_24848.diff
[CMD] [2020-12-03 11:51:34] tail -n +1 /app/public/converted_csv/moseley_moseley__refs_24848.csv >> /app/public/diff/moseley_moseley__refs_24848.diff
[CMD] [2020-12-03 11:51:34] echo "." >> /app/public/diff/moseley_moseley__refs_24848.diff
[CMD] [2020-12-03 11:51:34] echo "0a" > /app/public/diff/moseley_moseley__nodes_24849.diff
[CMD] [2020-12-03 11:51:34] tail -n +1 /app/public/converted_csv/moseley_moseley__nodes_24849.csv >> /app/public/diff/moseley_moseley__nodes_24849.diff
[CMD] [2020-12-03 11:51:34] echo "." >> /app/public/diff/moseley_moseley__nodes_24849.diff
[CMD] [2020-12-03 11:51:34] echo "0a" > /app/public/diff/moseley_moseley__occurrences_24850.diff
[CMD] [2020-12-03 11:51:34] tail -n +1 /app/public/converted_csv/moseley_moseley__occurrences_24850.csv >> /app/public/diff/moseley_moseley__occurrences_24850.diff
[CMD] [2020-12-03 11:51:34] echo "." >> /app/public/diff/moseley_moseley__occurrences_24850.diff
[CMD] [2020-12-03 11:51:34] echo "0a" > /app/public/diff/moseley_moseley__measurements_24851.diff
[CMD] [2020-12-03 11:51:34] tail -n +1 /app/public/converted_csv/moseley_moseley__measurements_24851.csv >> /app/public/diff/moseley_moseley__measurements_24851.diff
[CMD] [2020-12-03 11:51:34] echo "." >> /app/public/diff/moseley_moseley__measurements_24851.diff
[STOP] [2020-12-03 11:51:34] calculate_delta
[START] [2020-12-03 11:51:34] parse_diff_and_store
[INFO] [2020-12-03 11:51:34] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:51:34] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:51:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:51:34] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:51:35] Storing 6 ScientificNames
[INFO] [2020-12-03 11:51:35] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-03 11:51:35] Average Time: 0.0
[INFO] [2020-12-03 11:51:35] Total Time: 1s
[INFO] [2020-12-03 11:51:35] Storing 6 Nodes
[INFO] [2020-12-03 11:51:35] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-03 11:51:35] Average Time: 0.0
[INFO] [2020-12-03 11:51:35] Total Time: 1s
[INFO] [2020-12-03 11:51:35] Storing 6 Occurrences
[INFO] [2020-12-03 11:51:35] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-03 11:51:35] Average Time: 0.0
[INFO] [2020-12-03 11:51:35] Total Time: 1s
[INFO] [2020-12-03 11:51:35] Storing 22 Traits
[INFO] [2020-12-03 11:51:35] Processing group of 22 in 1 groups of 1000
[INFO] [2020-12-03 11:51:35] Average Time: 0.01
[INFO] [2020-12-03 11:51:35] Total Time: 1s
[INFO] [2020-12-03 11:51:35] Storing 11 MetaTraits
[INFO] [2020-12-03 11:51:35] Processing group of 11 in 1 groups of 1000
[INFO] [2020-12-03 11:51:35] Average Time: 0.0
[INFO] [2020-12-03 11:51:35] Total Time: 1s
[STOP] [2020-12-03 11:51:35] parse_diff_and_store
[START] [2020-12-03 11:51:35] resolve_keys
[INFO] [2020-12-03 11:51:40] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:51:40] traits to occurrences...
[INFO] [2020-12-03 11:51:40] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:51:40] Traits to sex term...
[INFO] [2020-12-03 11:51:40] Traits to lifestage term...
[INFO] [2020-12-03 11:51:40] MetaTraits to traits...
[INFO] [2020-12-03 11:51:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:51:40] Assocs to occurrences...
[INFO] [2020-12-03 11:51:40] Assocs to nodes...
[INFO] [2020-12-03 11:51:40] Assoc to sex term...
[INFO] [2020-12-03 11:51:40] Assoc to lifestage term...
[INFO] [2020-12-03 11:51:40] MetaAssoc to assocs...
[STOP] [2020-12-03 11:51:40] resolve_keys
[START] [2020-12-03 11:51:40] hold_for_later_1
[STOP] [2020-12-03 11:51:40] hold_for_later_1
[START] [2020-12-03 11:51:40] hold_for_later_2
[STOP] [2020-12-03 11:51:40] hold_for_later_2
[START] [2020-12-03 11:51:40] resolve_missing_parents
[STOP] [2020-12-03 11:51:40] resolve_missing_parents
[START] [2020-12-03 11:51:40] rebuild_nodes
[START] [2020-12-03 11:51:40] Flattener#flatten
[START] [2020-12-03 11:51:40] Flattener#study_resource
[START] [2020-12-03 11:51:40] Flattener#build_ancestry
[STOP] [2020-12-03 11:51:40] Flattener#build_ancestry
[INFO] [2020-12-03 11:51:40] 6 ancestry keys
[START] [2020-12-03 11:51:40] build_node_ancestors
[INFO] [2020-12-03 11:51:40] old ancestors deleted.
[STOP] [2020-12-03 11:51:40] build_node_ancestors
[WARN] [2020-12-03 11:51:40] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:51:40] Flattener#flatten
[STOP] [2020-12-03 11:51:40] rebuild_nodes
[START] [2020-12-03 11:51:40] resolve_missing_media_owners
[STOP] [2020-12-03 11:51:40] resolve_missing_media_owners
[START] [2020-12-03 11:51:40] sanitize_media_verbatims
[STOP] [2020-12-03 11:51:40] sanitize_media_verbatims
[START] [2020-12-03 11:51:40] queue_downloads
[STOP] [2020-12-03 11:51:40] queue_downloads
[START] [2020-12-03 11:51:40] parse_names
[WARN] [2020-12-03 11:51:40] I see 6 names which still need to be parsed.
[STOP] [2020-12-03 11:51:42] parse_names
[START] [2020-12-03 11:51:42] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:51:42] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:51:42] match_nodes
[START] [2020-12-03 11:51:42] map_all_nodes_to_pages
[STOP] [2020-12-03 11:51:42] map_all_nodes_to_pages
[INFO] [2020-12-03 11:51:42] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2020-12-03 11:51:42] update_nodes
[STOP] [2020-12-03 11:51:42] update_nodes
[STOP] [2020-12-03 11:51:42] match_nodes
[START] [2020-12-03 11:51:42] reindex_search
[STOP] [2020-12-03 11:51:42] reindex_search
[START] [2020-12-03 11:51:42] normalize_units
[STOP] [2020-12-03 11:51:42] normalize_units
[START] [2020-12-03 11:51:42] calculate_statistics
[2020-12-03 11:51:42] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:51:42] calculate_statistics
[START] [2020-12-03 11:51:42] complete_harvest_instance
[START] [2020-12-03 11:51:42] overall_tsv_creation
[INFO] [2020-12-03 11:51:42] Processing group of 6 in 1 batches of 10000
[INFO] [2020-12-03 11:52:21] 6 Traits (unfiltered)...
[INFO] [2020-12-03 11:52:59] 6 Traits (filtered)...
[INFO] [2020-12-03 11:52:59] 0 Associations (filtered)...
[INFO] [2020-12-03 11:52:59] 27 metadata added.
[INFO] [2020-12-03 11:52:59] 0 metadata added.
[INFO] [2020-12-03 11:52:59] Average Time: 54.62
[INFO] [2020-12-03 11:52:59] Total Time: 1m18s
[STOP] [2020-12-03 11:52:59] overall_tsv_creation
[INFO] [2020-12-03 11:52:59] Done. Check your files:
[INFO] [2020-12-03 11:52:59] (6 lines) /app/public/data/moseley_moseley_/publish_nodes.tsv
[INFO] [2020-12-03 11:52:59] (6 lines) /app/public/data/moseley_moseley_/publish_scientific_names.tsv
[INFO] [2020-12-03 11:52:59] (7 lines) /app/public/data/moseley_moseley_/publish_traits.tsv
[INFO] [2020-12-03 11:52:59] (28 lines) /app/public/data/moseley_moseley_/publish_metadata.tsv
[STOP] [2020-12-03 11:52:59] complete_harvest_instance
[START] [2020-12-03 11:52:59] completed
[STOP] [2020-12-03 11:52:59] completed
[STOP] [2020-12-03 11:52:59] logged process, took 87.12
[INFO] [2021-04-19 15:36:16] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:44:08] ## remove_type: ScientificName
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.778] Removed 6 Scientificnames
[INFO] [2021-04-19 15:44:08] ## remove_type: Vernacular
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.779] Removed 0 Vernaculars
[INFO] [2021-04-19 15:44:08] ## remove_type: Article
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.780] Removed 0 Articles
[INFO] [2021-04-19 15:44:08] ## remove_type: Medium
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.782] Removed 0 Media
[INFO] [2021-04-19 15:44:08] ## remove_type: Trait
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 22 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.784] Removed 22 Traits
[INFO] [2021-04-19 15:44:08] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 11 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.787] Removed 11 Metatraits
[INFO] [2021-04-19 15:44:08] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.789] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:44:08] ## remove_type: Assoc
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.790] Removed 0 Assocs
[INFO] [2021-04-19 15:44:08] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.792] Removed 0 Metaassocs
[INFO] [2021-04-19 15:44:08] ## remove_type: Identifier
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.793] Removed 0 Identifiers
[INFO] [2021-04-19 15:44:08] ## remove_type: Reference
[INFO] [2021-04-19 15:44:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:44:08] [15:44:08.795] Removed 0 References
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:08] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] Starting batch with ID 86116159...
[INFO] [2021-04-19 15:44:09] ## remove_type: Node
[INFO] [2021-04-19 15:44:09] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 15:44:09] [15:44:09.804] Removed 6 Nodes
[START] [2021-04-19 15:44:09] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:44:09] Creating resource from OpenData
[START] [2021-04-19 15:44:10] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:44:10] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:44:10] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:44:10] Creating resource from OpenData
[START] [2021-04-19 15:44:10] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:44:10] create_harvest_instance
[INFO] [2021-04-19 15:44:10] Created harvest instance #3776
[STOP] [2021-04-19 15:44:10] create_harvest_instance
[START] [2021-04-19 15:44:10] fetch_files
[STOP] [2021-04-19 15:44:10] fetch_files
[START] [2021-04-19 15:44:10] validate_each_file
[INFO] [2021-04-19 15:44:10] Looping over 4 formats...
[INFO] [2021-04-19 15:44:10] ...refs (/app/public/data/moseley_moseley_/references.tsv)
[INFO] [2021-04-19 15:44:10] Valid: /app/public/converted_csv/moseley_moseley__refs_3776.csv (0 lines)
[INFO] [2021-04-19 15:44:10] ...nodes (/app/public/data/moseley_moseley_/taxa.txt)
[INFO] [2021-04-19 15:44:10] Valid: /app/public/converted_csv/moseley_moseley__nodes_3776.csv (6 lines)
[INFO] [2021-04-19 15:44:10] ...occurrences (/app/public/data/moseley_moseley_/occurrences.txt)
[INFO] [2021-04-19 15:44:10] Valid: /app/public/converted_csv/moseley_moseley__occurrences_3776.csv (6 lines)
[INFO] [2021-04-19 15:44:10] ...measurements (/app/public/data/moseley_moseley_/measurementsorfacts.txt)
[INFO] [2021-04-19 15:44:10] Valid: /app/public/converted_csv/moseley_moseley__measurements_3776.csv (22 lines)
[STOP] [2021-04-19 15:44:10] validate_each_file
[START] [2021-04-19 15:44:10] convert_to_csv
[INFO] [2021-04-19 15:44:10] Looping over 4 formats...
[INFO] [2021-04-19 15:44:10] ...refs (/app/public/data/moseley_moseley_/references.tsv)
[CMD] [2021-04-19 15:44:10] /usr/bin/sort /app/public/converted_csv/moseley_moseley__refs_3776.csv > /app/public/converted_csv/moseley_moseley__refs_3776.csv_sorted
[INFO] [2021-04-19 15:44:10] Converted: /app/public/converted_csv/moseley_moseley__refs_3776.csv (0 lines)
[INFO] [2021-04-19 15:44:10] ...nodes (/app/public/data/moseley_moseley_/taxa.txt)
[CMD] [2021-04-19 15:44:10] /usr/bin/sort /app/public/converted_csv/moseley_moseley__nodes_3776.csv > /app/public/converted_csv/moseley_moseley__nodes_3776.csv_sorted
[INFO] [2021-04-19 15:44:10] Converted: /app/public/converted_csv/moseley_moseley__nodes_3776.csv (6 lines)
[INFO] [2021-04-19 15:44:10] ...occurrences (/app/public/data/moseley_moseley_/occurrences.txt)
[CMD] [2021-04-19 15:44:10] /usr/bin/sort /app/public/converted_csv/moseley_moseley__occurrences_3776.csv > /app/public/converted_csv/moseley_moseley__occurrences_3776.csv_sorted
[INFO] [2021-04-19 15:44:10] Converted: /app/public/converted_csv/moseley_moseley__occurrences_3776.csv (6 lines)
[INFO] [2021-04-19 15:44:10] ...measurements (/app/public/data/moseley_moseley_/measurementsorfacts.txt)
[CMD] [2021-04-19 15:44:10] /usr/bin/sort /app/public/converted_csv/moseley_moseley__measurements_3776.csv > /app/public/converted_csv/moseley_moseley__measurements_3776.csv_sorted
[INFO] [2021-04-19 15:44:10] Converted: /app/public/converted_csv/moseley_moseley__measurements_3776.csv (22 lines)
[STOP] [2021-04-19 15:44:10] convert_to_csv
[START] [2021-04-19 15:44:10] calculate_delta
[INFO] [2021-04-19 15:44:10] Looping over 4 formats...
[INFO] [2021-04-19 15:44:10] ...refs (/app/public/data/moseley_moseley_/references.tsv)
[CMD] [2021-04-19 15:44:10] echo "0a" > /app/public/diff/moseley_moseley__refs_3776.diff
[CMD] [2021-04-19 15:44:10] tail -n +1 /app/public/converted_csv/moseley_moseley__refs_3776.csv >> /app/public/diff/moseley_moseley__refs_3776.diff
[CMD] [2021-04-19 15:44:10] echo "." >> /app/public/diff/moseley_moseley__refs_3776.diff
[INFO] [2021-04-19 15:44:10] Created diff: /app/public/diff/moseley_moseley__refs_3776.diff (2 lines)
[INFO] [2021-04-19 15:44:10] ...nodes (/app/public/data/moseley_moseley_/taxa.txt)
[CMD] [2021-04-19 15:44:10] echo "0a" > /app/public/diff/moseley_moseley__nodes_3776.diff
[CMD] [2021-04-19 15:44:10] tail -n +1 /app/public/converted_csv/moseley_moseley__nodes_3776.csv >> /app/public/diff/moseley_moseley__nodes_3776.diff
[CMD] [2021-04-19 15:44:10] echo "." >> /app/public/diff/moseley_moseley__nodes_3776.diff
[INFO] [2021-04-19 15:44:10] Created diff: /app/public/diff/moseley_moseley__nodes_3776.diff (8 lines)
[INFO] [2021-04-19 15:44:10] ...occurrences (/app/public/data/moseley_moseley_/occurrences.txt)
[CMD] [2021-04-19 15:44:10] echo "0a" > /app/public/diff/moseley_moseley__occurrences_3776.diff
[CMD] [2021-04-19 15:44:10] tail -n +1 /app/public/converted_csv/moseley_moseley__occurrences_3776.csv >> /app/public/diff/moseley_moseley__occurrences_3776.diff
[CMD] [2021-04-19 15:44:10] echo "." >> /app/public/diff/moseley_moseley__occurrences_3776.diff
[INFO] [2021-04-19 15:44:10] Created diff: /app/public/diff/moseley_moseley__occurrences_3776.diff (8 lines)
[INFO] [2021-04-19 15:44:10] ...measurements (/app/public/data/moseley_moseley_/measurementsorfacts.txt)
[CMD] [2021-04-19 15:44:10] echo "0a" > /app/public/diff/moseley_moseley__measurements_3776.diff
[CMD] [2021-04-19 15:44:10] tail -n +1 /app/public/converted_csv/moseley_moseley__measurements_3776.csv >> /app/public/diff/moseley_moseley__measurements_3776.diff
[CMD] [2021-04-19 15:44:10] echo "." >> /app/public/diff/moseley_moseley__measurements_3776.diff
[INFO] [2021-04-19 15:44:10] Created diff: /app/public/diff/moseley_moseley__measurements_3776.diff (24 lines)
[STOP] [2021-04-19 15:44:10] calculate_delta
[START] [2021-04-19 15:44:10] parse_diff_and_store
[INFO] [2021-04-19 15:44:10] Handling diff: /app/public/diff/moseley_moseley__refs_3776.diff (2 lines)
[INFO] [2021-04-19 15:44:10] Loading refs diff file into memory (2 /app/public/diff/moseley_moseley__refs_3776.diff lines)...
[INFO] [2021-04-19 15:44:10] Handling diff: /app/public/diff/moseley_moseley__nodes_3776.diff (8 lines)
[INFO] [2021-04-19 15:44:10] Loading nodes diff file into memory (8 /app/public/diff/moseley_moseley__nodes_3776.diff lines)...
[INFO] [2021-04-19 15:44:10] Handling diff: /app/public/diff/moseley_moseley__occurrences_3776.diff (8 lines)
[INFO] [2021-04-19 15:44:10] Loading occurrences diff file into memory (8 /app/public/diff/moseley_moseley__occurrences_3776.diff lines)...
[INFO] [2021-04-19 15:44:10] Handling diff: /app/public/diff/moseley_moseley__measurements_3776.diff (24 lines)
[INFO] [2021-04-19 15:44:10] Loading measurements diff file into memory (24 /app/public/diff/moseley_moseley__measurements_3776.diff lines)...
[INFO] [2021-04-19 15:44:10] Storing 6 ScientificNames
[INFO] [2021-04-19 15:44:10] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 15:44:10] Average Time: 0.0
[INFO] [2021-04-19 15:44:10] Total Time: 1s
[INFO] [2021-04-19 15:44:10] Storing 6 Nodes
[INFO] [2021-04-19 15:44:10] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 15:44:10] Average Time: 0.0
[INFO] [2021-04-19 15:44:10] Total Time: 1s
[INFO] [2021-04-19 15:44:10] Storing 6 Occurrences
[INFO] [2021-04-19 15:44:10] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 15:44:10] Average Time: 0.0
[INFO] [2021-04-19 15:44:10] Total Time: 1s
[INFO] [2021-04-19 15:44:10] Storing 22 Traits
[INFO] [2021-04-19 15:44:10] Processing group of 22 in 1 groups of 1000
[INFO] [2021-04-19 15:44:10] Average Time: 0.01
[INFO] [2021-04-19 15:44:10] Total Time: 1s
[INFO] [2021-04-19 15:44:10] Storing 11 MetaTraits
[INFO] [2021-04-19 15:44:10] Processing group of 11 in 1 groups of 1000
[INFO] [2021-04-19 15:44:10] Average Time: 0.0
[INFO] [2021-04-19 15:44:10] Total Time: 1s
[STOP] [2021-04-19 15:44:10] parse_diff_and_store
[START] [2021-04-19 15:44:10] resolve_keys
[INFO] [2021-04-19 15:44:16] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:44:16] traits to occurrences...
[INFO] [2021-04-19 15:44:16] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:44:16] Traits to sex term...
[INFO] [2021-04-19 15:44:16] Traits to lifestage term...
[INFO] [2021-04-19 15:44:16] MetaTraits to traits...
[INFO] [2021-04-19 15:44:16] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:44:16] Assocs to occurrences...
[INFO] [2021-04-19 15:44:16] Assocs to nodes...
[INFO] [2021-04-19 15:44:16] Assoc to sex term...
[INFO] [2021-04-19 15:44:16] Assoc to lifestage term...
[INFO] [2021-04-19 15:44:16] MetaAssoc to assocs...
[STOP] [2021-04-19 15:44:16] resolve_keys
[START] [2021-04-19 15:44:16] hold_for_later_1
[STOP] [2021-04-19 15:44:16] hold_for_later_1
[START] [2021-04-19 15:44:16] hold_for_later_2
[STOP] [2021-04-19 15:44:16] hold_for_later_2
[START] [2021-04-19 15:44:16] resolve_missing_parents
[STOP] [2021-04-19 15:44:16] resolve_missing_parents
[START] [2021-04-19 15:44:16] rebuild_nodes
[START] [2021-04-19 15:44:16] Flattener#flatten
[START] [2021-04-19 15:44:16] Flattener#study_resource
[START] [2021-04-19 15:44:16] Flattener#build_ancestry
[STOP] [2021-04-19 15:44:16] Flattener#build_ancestry
[INFO] [2021-04-19 15:44:16] 6 ancestry keys
[START] [2021-04-19 15:44:16] build_node_ancestors
[INFO] [2021-04-19 15:44:16] old ancestors deleted.
[STOP] [2021-04-19 15:44:16] build_node_ancestors
[WARN] [2021-04-19 15:44:16] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:44:16] Flattener#flatten
[STOP] [2021-04-19 15:44:16] rebuild_nodes
[START] [2021-04-19 15:44:16] resolve_missing_media_owners
[STOP] [2021-04-19 15:44:16] resolve_missing_media_owners
[START] [2021-04-19 15:44:16] sanitize_media_verbatims
[STOP] [2021-04-19 15:44:16] sanitize_media_verbatims
[START] [2021-04-19 15:44:16] queue_downloads
[STOP] [2021-04-19 15:44:16] queue_downloads
[START] [2021-04-19 15:44:16] parse_names
[WARN] [2021-04-19 15:44:16] I see 6 names which still need to be parsed.
[STOP] [2021-04-19 15:44:17] parse_names
[START] [2021-04-19 15:44:17] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:44:17] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:44:17] match_nodes
[START] [2021-04-19 15:44:17] map_all_nodes_to_pages
[STOP] [2021-04-19 15:44:17] map_all_nodes_to_pages
[INFO] [2021-04-19 15:44:17] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2021-04-19 15:44:17] update_nodes
[STOP] [2021-04-19 15:44:17] update_nodes
[STOP] [2021-04-19 15:44:17] match_nodes
[START] [2021-04-19 15:44:17] reindex_search
[STOP] [2021-04-19 15:44:17] reindex_search
[START] [2021-04-19 15:44:17] normalize_units
[STOP] [2021-04-19 15:44:17] normalize_units
[START] [2021-04-19 15:44:17] calculate_statistics
[2021-04-19 15:44:17] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:44:17] calculate_statistics
[START] [2021-04-19 15:44:17] complete_harvest_instance
[START] [2021-04-19 15:44:17] overall_tsv_creation
[INFO] [2021-04-19 15:44:17] Processing group of 6 in 1 batches of 10000
[INFO] [2021-04-19 15:44:53] 6 Traits (unfiltered)...
[INFO] [2021-04-19 15:45:26] 6 Traits (filtered)...
[INFO] [2021-04-19 15:45:26] 0 Associations (filtered)...
[INFO] [2021-04-19 15:45:26] 16 metadata added.
[INFO] [2021-04-19 15:45:26] 0 metadata added.
[INFO] [2021-04-19 15:45:52] Average Time: 71.17
[INFO] [2021-04-19 15:45:52] Total Time: 1m35s
[STOP] [2021-04-19 15:45:52] overall_tsv_creation
[INFO] [2021-04-19 15:45:52] Done. Check your files:
[INFO] [2021-04-19 15:45:52] (6 lines) /app/public/data/moseley_moseley_/publish_nodes.tsv
[INFO] [2021-04-19 15:45:52] (6 lines) /app/public/data/moseley_moseley_/publish_scientific_names.tsv
[INFO] [2021-04-19 15:45:52] (7 lines) /app/public/data/moseley_moseley_/publish_traits.tsv
[INFO] [2021-04-19 15:45:52] (17 lines) /app/public/data/moseley_moseley_/publish_metadata.tsv
[STOP] [2021-04-19 15:45:52] complete_harvest_instance
[START] [2021-04-19 15:45:52] completed
[STOP] [2021-04-19 15:45:52] completed
[STOP] [2021-04-19 15:45:52] logged process, took 102.7

Latest Process